We’ve had several customers who have been surprised that JMP Genomics can handle high-throughput data generated on non-array platforms. These customers and others are glad to hear that JMP Genomics can also handle TaqMan data, processed NextGen sequencing data, and data generated on custom array platforms or other commercial platforms (e.g., Agilent, Phalanx Biotech). You can usually import these data sets easily into JMP Genomics for processing and analysis using many of the same tools as for expression or genotyping analysis.
You may have noticed increasing support for Affymetrix formats (CEL and CHP for expression and SNP, CNCHP, ARRs, and download from NetAffx) and Illumina BeadStudio outputs (Expression, SNP, Copy Number) in JMP Genomics over the past few releases. The flexible text import processes we also include allow import of your text files (even very wide text files) into JMP Genomics as single files or multiple files to be compiled into one large data file. Perhaps this is a point we need to make more strongly to customers and prospects. We can handle more than just your array data! Check it out, and you will be pleasantly surprised what you can do.